I was successfully able to build the JAR file and repository.xml file under the downloads section of the bitbucket. Also, tested the downloads path with IGB platform.
I have transferred the ownership of the repository to 'lorainelab'.
You can check the repository on the following path:
https://bitbucket.org/pkulka10/protannot/src/master/
If you are accessing the repo after accepting the ownership for it then instead of 'pkulka10' you just need to add 'lorainelab'.

Prof. [~aloraine] I changed the pom as well as the pipeline configuration file of protannot app. I found some dependencies which are not being used by the app. So, I went ahead and commented those dependencies just to check if the app works fine without those dependencies. I tested both apps, the existing one and the latest one which is built using the new repository. Also, I compared the results for InterProScan of both the apps and they are identical. Shall I delete that part of the code? Please let me know.
Below are the artifactIds of the dependencies which are not being used :
freehep-graphicsio-svg
commons-compress
logback-core
logback-classic
guava

I think freehep-graphicsio-svg is being used to creates images, but the code itself (I thought) is coming from the platform. I would say: go ahead and delete it from the POM, but check that you can save an image from the ProtAnnot. Depending on how the wiring is done, you might see class not found errors (OSGi related).

To test:

• De-activate igbserver app repository
• Install App from Downloads URL of bitbucket repo - https://bitbucket.org/lorainelab/protannot/downloads/
• Launch IGB, select at least one gene model
• Choose Tools > ProtAnnot
• Operate the menu options: Make an image of the view, save data to an XML file, check that you can open it again.

The above functionality may depend on the libraries that have been removed from the project.

The repository for ProtAnnot has been tested successfully. The app is working as expected. Moving to closed.